REPORTE DE MUESTRA
- Nombre
- Thalassomics
- Contacto
- info@thalassomics.com
- Sitio Web
- https://github.com/trippv/integrity_massively
- Tipo de proyecto
- RNA-seq
- Platafora
- HiSeq 2500 High Output V4
- Setup
- 2x125
General Statistics
| Sample Name | % Duplication | % > Q30 | Mb Q30 bases | Reads After Filtering | GC content | % PF | % Adapter | Frag Length | % Aligned | M Aligned |
|---|---|---|---|---|---|---|---|---|---|---|
| batch1_R1 | 167.6bp | 99.9% | 0.0M | |||||||
| batch1_chrI | 0.0% | 92.8% | 7.6Mb | 0.1M | 43.4% | 99.4% | 1.5% | |||
| batch2_R1 | 170.8bp | 99.9% | 0.1M | |||||||
| batch2_chrI | 0.0% | 92.9% | 10.6Mb | 0.1M | 43.4% | 100.0% | 0.6% | |||
| batch3_R1 | 167.4bp | 99.9% | 0.0M | |||||||
| batch3_chrI | 0.0% | 92.8% | 8.1Mb | 0.1M | 43.6% | 99.5% | 1.4% | |||
| chem1_R1 | 166.8bp | 99.9% | 0.0M | |||||||
| chem1_chrI | 0.0% | 92.9% | 6.7Mb | 0.1M | 43.4% | 100.0% | 0.7% | |||
| chem2_R1 | 172.5bp | 99.9% | 0.0M | |||||||
| chem2_chrI | 0.0% | 93.1% | 8.4Mb | 0.1M | 43.3% | 100.0% | 0.5% | |||
| chem3_R1 | 173.5bp | 99.9% | 0.1M | |||||||
| chem3_chrI | 0.0% | 93.1% | 10.1Mb | 0.1M | 43.4% | 100.0% | 0.6% |
fastp
0.23.4
All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560
Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
BUSCO
5.8.2
Assesses genome assembly and annotation completeness.URL: http://busco.ezlab.orgDOI: 10.1093/bioinformatics/btv351
BUSCO v2 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.Lineage: eukaryota_odb10
Kallisto
Quantifies abundances of transcripts (or more generally, of target sequences) from RNA-Seq data.URL: http://pachterlab.github.io/kallistoDOI: 10.1038/nbt.3519
Pca Plot
Análisis de Expresión Diferencial
PCA de expresión génica
El gráfico de PCA (Análisis de Componentes Principales) permite visualizar cómo se agrupan las muestras según su perfil de expresión génica. Muestras cercanas entre sí tienen patrones de expresión similares, lo que puede reflejar similitudes biológicas o técnicas entre los grupos.
Expresión diferencial
El volcano plot muestra los genes diferencialmente expresados entre dos grupos. Cada punto representa un gen: el eje X indica el cambio en la expresión (log₂ Fold Change), y el eje Y indica la significancia estadística (-log₁₀ p-valor ajustado). Los genes más alejados y en rojo son los más significativamente regulados.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| BUSCO | 5.8.2 |
| fastp | 0.23.4 |